Student Publications
2024
Kafi Belfon
Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate https://pubs.acs.org/doi/10.1021/acs.biochem.3c00640
Yu-Ching Chen
Uncovering the roles of Mycobacterium tuberculosis melH in redox and bioenergetic homeostasis: implications for antitubercular therapy https://journals.asm.org/doi/10.1128/msphere.00061-24
Brandon Irizarry
An electrostatic cluster guides Aβ40 fibril formation in sporadic and Dutch-type cerebral amyloid angiopathy https://www.sciencedirect.com/science/article/pii/S1047847724000327?via%3Dihub
Pavana Suresh
Linking insulin receptor activation to hydrophobic mismatch using transmembrane mutations https://www.cell.com/biophysj/fulltext/S0006-3495(23)01432-7
MαCD-based plasma membrane outer leaflet lipid exchange in mammalian cells to study insulin receptor activity https://www.sciencedirect.com/science/article/pii/S0076687924001228?via%3Dihub
2023
Kafi Belfon
Structure-Guided Discovery of N5-CAIR Mutase Inhibitors https://pubs.acs.org/doi/10.1021/acs.biochem.2c00705
Yu-Ching Chen
A Chemoproteomic Approach to Elucidate the Mechanism of Action of 6-Azasteroids with Unique Activity in Mycobacteria https://doi.org/10.1021/acsinfecdis.3c00296
Yong-Mi Choi
Structural insights into perilipin 3 membrane association in response to diacylglycerol accumulation https://www.nature.com/articles/s41467-023-38725-w
Ming-Hao Li
Interspecies Variation Affects Islet Amyloid Polypeptide Membrane Binding https://pubs.acs.org/doi/10.1021/acs.biochem.2c00470
Impact of Ca2+ on membrane catalyzed IAPP amyloid formation and IAPP induced vesicle leakage https://www.sciencedirect.com/science/article/pii/S0005273623000433
2022
Forrest Bowling
Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB https://www.embopress.org/doi/full/10.15252/embj.2022110698
Yong-Mi Choi
Structure and Dynamics of Human Perilipin 3 Membrane Association https://faseb.onlinelibrary.wiley.com/doi/10.1096/fasebj.2022.36.S1.00R88
Measurement of neutral ceramidase activity in vitro and in vivo https://www.sciencedirect.com/science/article/abs/pii/S000326972200032X?via%3Dihub
Ming-Hao Li
Analysis of Sheep and Goat IAPP Provides Insight into IAPP Amyloidogenicity and Cytotoxicity https://pubs.acs.org/doi/10.1021/acs.biochem.2c00470
Lauren Prentis
A molecular evolution algorithm for ligand design in DOCK https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26993
Pavana Suresh
Effect of MαCD-mediated phospholipid exchange on plasma membrane ordered lipid domain stability https://www.cell.com/biophysj/fulltext/S0006-3495(21)02841-1
Alexandra Weinheimer
Extended DNA binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks https://doi.org/10.1016/j.jbc.2022.102268
2021
Forrest Bowling
Structure and regulation of human phospholipase D https://www.sciencedirect.com/science/article/abs/pii/S2212492620300944?via%3Dihub
Brandon Irizarry
Human cerebral vascular amyloid contains both antiparallel and parallel in-register Aβ40 fibrils https://www.sciencedirect.com/science/article/pii/S0021925821010620?via%3Dihub
Ming-Hao Li
Preparation of Asymmetric Vesicles with Trapped CsCl Avoids Osmotic Imbalance, Non-Physiological External Solutions, and Minimizes Leakage https://pubs.acs.org/doi/10.1021/acs.langmuir.1c01971
The Fluorescent Dye 1,6-Diphenyl-1,3,5-hexatriene Binds to Amyloid Fibrils Formed by Human Amylin and Provides a New Probe of Amylin Amyloid Kinetics https://pubs.acs.org/doi/10.1021/acs.biochem.1c00328
Frank Mindlin
Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer https://www.sciencedirect.com/science/article/pii/S002228362030718X
Pavana Suresh
Loss of plasma membrane lipid asymmetry can induce ordered domain (raft) formation https://www.sciencedirect.com/science/article/pii/S0022227521001383?via%3Dihub
Using cyclodextrin-induced lipid substitution to study membrane lipid and ordered membrane domain (raft) function in cells https://www.sciencedirect.com/science/article/pii/S0005273621002224?via%3Dihub
Phospholipid exchange shows insulin receptor activity is supported by both the propensity to form wide bilayers and ordered raft domains https://www.sciencedirect.com/science/article/pii/S0021925821008127?via%3Dihub
Modulation of Insulin Receptor Activity Upon Plasma Membrane Sterol and Phospholipid Substitutions to Alter Lipid Domain Formation https://www.sciencedirect.com/science/article/pii/S0006349520329660?via%3Dihub
2020
Forrest Bowling
Crystal structure of human PLD1 provides insight into activation by PI(4,5)P2 and RhoA https://www.nature.com/articles/s41589-020-0499-8
Yong-Mi Choi
Identification of Small-Molecule Inhibitors of Neutral Ceramidase (nCDase) via Target-Based High-Throughput Screening https://www.sciencedirect.com/science/article/pii/S247255522206659X?via%3Dihub
Valerie Khayyo
Crystal structure of a lipin/Pah phosphatidic acid phosphatase https://www.nature.com/articles/s41467-020-15124-z
Daeun Noh
Analysis of Amylin Consensus Sequences Suggests That Human Amylin Is Not Optimized to Minimize Amyloid Formation and Provides Clues to Factors That Modulate Amyloidogenicity https://pubs.acs.org/doi/10.1021/acschembio.9b01050
Analysis of Proline Substitutions Reveals the Plasticity and Sequence Sensitivity of Human IAPP Amyloidogenicity and Toxicity https://pubmed.ncbi.nlm.nih.gov/31922743/
Alexandra Weinheimer
SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks https://www.nature.com/articles/s41467-020-19162-5
2019
Frank Mindlin
Structure of the full-length Clostridium difficile toxin B https://www.nature.com/articles/s41594-019-0268-0
Daeun Noh
Analysis of Prairie Vole Amylin Reveals the Importance of the N-Terminus and Residue 22 in Amyloidogenicity and Cytotoxicity https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254015/
Lauren Prentis
FABP1 controls hepatic transport and biotransformation of Δ9-THC https://www.nature.com/articles/s41598-019-44108-3
Alexandra Weinheimer
Proteolytic Control of Genome Integrity at the Replication Fork https://pubmed.ncbi.nlm.nih.gov/31324531/
Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks https://academic.oup.com/nar/article/47/8/3996/5304317
2018
Bezalel Bacon
Bacterial haemoprotein sensors of NO: H-NOX and NosP https://www.sciencedirect.com/science/article/pii/S0065291117300048
Bacterial Heme-Based Sensors of Nitric Oxide. Antioxidants & Redox Signaling https://www.liebertpub.com/doi/full/10.1089/ars.2017.7235
Frank Mindlin
Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95 https://www.nature.com/articles/s41467-018-06133-0
2017
Sanchez-Reyes OB, Cooke ALG, Tranter DB, Rashid D, Eilers M, Reeves PJ, Smith SO. Biophys J. 2017 Jun 6;112(11):2315-2326. doi: 10.1016/j.bpj.2017.04.051.
Chitrakar, I., Kim-Holzapfel, D.M., Zhou, W. and French, J.B. (2017) Higher Order Structures in Purine and Pyrimidine Metabolism. J. Struct. Biol. 197(3): 354-364.
WeberFishkin, S., Clark, R., Galanakis, D., Irizarry, B., Young, A. and Frame, M. (2017) Fibrinogen and its Soluble Fibrin as Mediators of Erythrocyte Aggregation. FASEB Abstract Number:677.6
Yasunori Noguchi(*), Zuanning Yuan(*), Lin Bai(*), Sarah Schneider, Bruce Stillman, Christian Speck, and Huilin Li Cryo-EM structure of Mcm2-7 double-hexamer on DNA suggests a lagging strand DNA extrusion model (2017)Proc. Natl. Acad. Sci. U S A. 114(45) * co-first author
Zuanning Yuan, Lin Bai, Alberto Riera, Jingchuan Sun, Bruce Stillman, Christian Speck, and Huilin Li Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. (2017) Nature Structural & Molecular biology 24(3):316-324
Ante Tocilj, Kin Fan On, Zuanning Yuan, Jingchuan Sun, Elad Elkayam, Huilin Li, Bruce Stillman, Leemor Joshua-Tor Structure of the active form of human Origin Recognition Complex and its ATPase motor module (2017) eLife 6:e20818)
Roxana Georgescu*, Zuanning Yuan*, Lin Bai*, Ruda de Luna Almeida Santos, Jingchuan Sun, Dan Zhang, Olga Yurieva, Huilin Li and Michael E. O’Donnell Structure of Eukaryotic CMG Helicase at a Replication Fork and Implications to Replisome Architecture and Origin Initiation (2017) Proc. Natl. Acad. Sci. U S A. 113(48):13612-13617)* co-first author
Georgescu, R. , Yuan, Z., Bai, L., Santos, R.L.A., Sun, J., Zhang, D., Yurieva, O., Li, H., O’Donnell, M.E. (2017) Structure of CMG
helicase at a replication fork.Proc. Natl. Acad. Sci. U S A. 114 (5), E697-E706.
Santos, R.L.A., Bai, L., Singh, P.K., Murakami, N., Fan, H., Zhan, W., Zhu, Y., Jiang, X., Zhang,
K., Assker, J.P., Nathan, F.C., Li, H., Azzi, J., Lin, G. (2017) Structure of human
immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits
activated lymphocytes. Nature Communications 8(1):1692.
St Clair, J. R. S., Wang, Q., Li, G., & London, E. (2017). Preparation and Physical Properties of Asymmetric
Model Membrane Vesicles. In The Biophysics of Cell Membranes (pp. 1-27). Springer, Singapore.
Zhang, X., St. Clair, J. R., London, E., & Raleigh, D. P. (2017). Islet amyloid polypeptide membrane interactions:
Effects of membrane composition. Biochemistry, 56(2), 376-390.
Shek, R., Dattmore, D. A., Stives, D. P., Jackson, A. L., Chatfield, C. H., Hicks, K. A., and French, J. B. (2017) Structural and functional basis for targeting Campylobacter jejuni agmatine deiminase to overcome antibiotic resistance, Biochemistry 56, 6734-6742
2016
Li, G., Kim, J., Huang, Z., Clair, J. R. S., Brown, D. A., & London, E. (2016). Efficient replacement of plasma membrane outer
leaflet phospholipids and sphingolipids in cells with exogenous lipids. Proc. Natl. Acad. Sci. U S A., 113(49), 14025-14030.
Zuanning Yuan, Lin Bai, Jingchuan Sun, Roxana Georgescu, Jun Liu, Michael E. O’Donnell, Huilin Li Structure of the eukaryotic replicative CMG helicase and pumpjack motion (2016) Nature Structural & Molecular Biology23(3):217-24
2015
Yang, M., Lu, R., Guja, K. E., Wipperman, M. F., St. Clair, J. R., Bonds, A. C., ... & Sampson, N. S. (2015). Unraveling cholesterol catabolism in Mycobacterium tuberculosis: ChsE4-ChsE5 α2β2 acyl-CoA dehydrogenase initiates β-oxidation of 3-oxo-cholest-4-en-26-oyl CoA. ACS Infectious Diseases, 1(2), 110-125.
Chen YC, Wu YT, and Wei YH. (2015) Depletion of mitoferrins leads to mitochondrial dysfunction and impairment of adipogenic differentiation in 3T3-L1 preadipocytes. Free Radic Res. 49(11):1285-95.
Jingchuan Sun, Yi Shi, Roxana E Georgescu, Zuanning Yuan, Brian T Chait, Huilin Li &Michael E O’Donnell The architecture of a eukaryotic replisome (2015) Nature Structural & Molecular Biology.22(12):976-82
Matarlo, J. S., Evans, C. E., Sharma, I., Lavaud, L. J., Ngo, S. C., Shek, R., Rajashankar, K. R., French, J. B., Tan, D. S., and Tonge, P. J. (2015) Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents, Biochemistry 54, 6514.
2014
Jingchuan Sun, Alejandra Fernandez-Cid, Alberto Riera, Silvia Tognetti, Zuanning Yuan, Bruce Stillman, Christian Speck, Huilin Li Structural and mechanistic insights into Mcm2–7 double-hexamer assembly and function (2014) Genes & Development. 28: 2291-2303
2012
Li CJ, Huang SY, Wu MY, Chen YC, Tsang SF, Chyuan JH,and Hsu HY. (2012) Induction of apoptosis by ethanolic extract of Corchorus olitorius leaf in human hepatocellular carcinoma (HepG2) cells via a mitochondria-dependent pathway. Molecules 3;17(8):9348-60.